* One or more symlinks to directories have been preserved in order to
* ensure that files installed via these symlinks remain accessible. This
* indicates that the mentioned symlink(s) may be obsolete remnants of an
* old install, and it may be appropriate to replace a given symlink with
* the directory that it points to.
*
* /var/run
*

You probably want to keep that /var/run symlink, at least until all of
your installed packages have been fixed to use /run directly. You can
suppress the warning by putting a setting like this in make.conf: